Variant report

Variant	rs3776165
Chromosome Location	chr5:100188616-100188617
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:100187668..100190190-chr5:100190255..100193150,3	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10515265	1.00[EUR][1000 genomes]
rs10515266	1.00[EUR][1000 genomes]
rs1423381	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17159344	1.00[EUR][1000 genomes]
rs17159370	1.00[EUR][1000 genomes]
rs17159464	1.00[EUR][1000 genomes]
rs17159467	1.00[EUR][1000 genomes]
rs17159519	1.00[EUR][1000 genomes]
rs17159602	1.00[EUR][1000 genomes]
rs17159616	1.00[EUR][1000 genomes]
rs17159626	1.00[EUR][1000 genomes]
rs17160705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17160732	1.00[CEU][hapmap];0.98[AMR][1000 genomes]
rs17160771	1.00[GIH][hapmap];0.85[MEX][hapmap]
rs17160844	1.00[CEU][hapmap];0.89[MEX][hapmap];0.94[AMR][1000 genomes]
rs17161136	0.87[AMR][1000 genomes]
rs2544911	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2544912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs2544914	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2544915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2544916	0.96[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2544917	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2544919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2548272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548275	0.88[AMR][1000 genomes]
rs2548277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2561524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2561525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2561526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2561527	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2725118	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2725123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3776166	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776172	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs3776173	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs3776179	0.88[ASN][1000 genomes]
rs3857364	1.00[EUR][1000 genomes]
rs6595534	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes]
rs6897681	1.00[EUR][1000 genomes]
rs73162282	0.88[ASN][1000 genomes]
rs73775624	1.00[EUR][1000 genomes]
rs768777	1.00[EUR][1000 genomes]
rs980901	1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021183	chr5:99625857-100221426	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	nsv1023765	chr5:99915011-100733755	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	esv1834675	chr5:100143084-100535029	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv980990	chr5:100183442-100190408	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100147600-100218000	Weak transcription	Thymus	Thymus
2	chr5:100174000-100190600	Weak transcription	Fetal Lung	lung
3	chr5:100177600-100215400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:100177800-100188800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:100178200-100218400	Weak transcription	Placenta	Placenta
6	chr5:100185800-100190400	Weak transcription	Fetal Thymus	thymus
7	chr5:100187000-100199200	Weak transcription	Lung	lung
8	chr5:100187200-100192800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:100187400-100190600	Enhancers	Primary hematopoietic stem cells	blood
10	chr5:100187800-100188800	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr5:100187800-100189800	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr5:100187800-100190800	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr5:100187800-100191000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr5:100187800-100192400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:100187800-100193000	Enhancers	Primary B cells from peripheral blood	blood
16	chr5:100188000-100189400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr5:100188000-100190400	Enhancers	Primary T cells from cord blood	blood
18	chr5:100188200-100189200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr5:100188200-100190800	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr5:100188200-100191400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr5:100188200-100192200	Weak transcription	Spleen	Spleen
22	chr5:100188200-100192800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr5:100188400-100188800	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr5:100188400-100188800	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr5:100188400-100189800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr5:100188400-100191000	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr5:100188400-100192200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:100188400-100192200	Weak transcription	Brain Germinal Matrix	brain
29	chr5:100188400-100194600	Strong transcription	Dnd41	blood
30	chr5:100188600-100188800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr5:100188600-100189000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:100188600-100189200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr5:100188600-100189200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:100188600-100189200	Active TSS	GM12878-XiMat	blood
35	chr5:100188600-100189600	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr5:100188600-100190400	Enhancers	HUVEC	blood vessel
37	chr5:100188600-100191600	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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